First up we see our three heroes in a park with an apple tree. Pikachu is standing behind some bushes next to the tree. Suddenly it falls down as if it is dead. Brock and Misty see this but Ash doesn't since he was sleeping. Brock races over to get Pikachu while Misty tries to wake up Ash. Brock runs over to Ash and Misty with Pikachu in his arms. He says that there might be something stuck in Pikachu's throat that is making its voice weird. He then says that they have to get Pikachu to a Pokémon Center very quickly. Ash tries shaking Pikachu to get its throat clear but it doesn't work.
Ash and friends then run down the path looking for the nearest Pokémon Center. Brock says that there isn't a Pokémon Center for miles around. They reach a hospital, a human one, and start knocking on the door and crying out for help. The doctor comes to the door complain about not getting enough sleep. Ash says that his Pikachu needs help fast. It is an emergency. Misty then says the same thing and the doctor says that he can't resist a pretty face.
The doctor takes Ash, Misty, Brock and Pikachu inside. He says that treating Pokémon is not his specialty and that they should go see Nurse Joy at the Pokémon Center. They say that it is too far and Pikachu wouldn't make it. After telling them that his name is Dr. Procter, he agrees to help. He takes Pikachu into his operating theater. Pikachu has already fainted by now. Dr. Proctor puts a stethoscope to Pikachu's throat. He says that there is something stuck in it. He hooks up a machine to Pikachu's cheeks which tells him that Pikachu's electric pressure is low. He asks Brock to get the fribulator (machine that shocks people so that there hearts start beating) and set it to 10,000 volts. He then grabs the two ends of the machine and yells, "Clear!" The two ends are put onto Pikachu for a second and an electric shock gets Pikachu. Pikachu now wakes up. Dr. Proctor asks it to open its mouth so he can get its throat clear. Pikachu does so and Dr. Proctor reaches into Pikachu's mouth and gets shocked, but he still manages to pull out an entire apple. Dr. Proctor says that Ash is a bad trainer to let his Pikachu eat an apple whole. Ash protests saying that he didn't let Pikachu eat it. Suddenly the phone starts to ring. Dr. Proctor says that he is off duty and won't answer it. Brock ends up answering the phone. It’s Nurse Joy. She says there has been an accident and she needs the extra room of the hospital to help treat Pokémon. She then shows a video of a crash scene with Pokémon scattered everywhere. Jessie and James are there too fighting over who was supposed to be watching the road. James says he thought Meowth was. Meowth is sitting down crying because he can't find the charm that is supposed to be on his head. Nurse Joy says that they need help urgently. Dr. Proctor asks f she would like to go out and get pizza with him sometime. Nurse Joy gets angry at him and he says that you can't blame a guy for trying. Brock says he doesn't like Dr. Proctor because he sounds to much like himself. Misty agrees. Dr. Proctor hands everyone hospital uniforms and some equipment. He says he needs help because there are not enough doctor and nurses.
Suddenly they hear an ambulance coming. Two Chansey carry in a stretcher carrying a crying Cubone. They put it onto the operating table and hand Dr. Proctor some X-rays. Ash sends out Bulbasaur to hold down Cubone. Dr. Proctor says you can't be to rough with patients. He then says that Cubone has fractures that will have to be repaired with super glue and a bandage. Misty picks it up and says that it will be all right. The Cubone then calms down. Dr. Proctor say that Misty is a natural.
The next patients are brought in by Jessie and James. They have and Arbok and a Raticate. Jessie is really mad because the Raticate is trying to bite her Arbok. Dr. Proctor says that it can't since it has broken teeth. He orders that it has them glued back on with the almighty super glue. Dr. Proctor then asks Jessie if she wants to go out for some pizza sometime. Jessie has hearts in her eyes and says that Dr. Proctor must be a very good doctor. Dr. Proctor says he will help her Arbok. He says that Arbok poison is circulating around its body. He takes it over to Ash who says that he shouldn't help them because they are from Team Rocket. Dr. Proctor gives Arbok a shot of anesthetic and Jessie yells at him saying you are supposed to heal it, not kill it. Dr. Proctor explains that it is only sleeping not dead. Ash asks him why he is helping Team Rocket. He says that doctors are not here to judge but to heal. He then says that maybe he can convince this beautiful young lady to help. Jessie says that he is obviously referring to me. We will help as best as we can.
Next we see Meowth on a hospital bed still crying over his lost charm. It says it will pay any price to get it back. The nearby Chansey hands him a bowl of rice. Meowth yells at it, "Price not rice!" The Chansey then hands it a game, but Meowth says that it doesn't want to play. Chansey tries to cheer up Meowth. It even gives it the Officer Jenny's booth from Pokémon Emergency! Chansey then tries giving the tiresome Meowth a Venonat, but still Meowth was sad. Meowth then goes a bit crazy so Chansey slaps its face then applies a bandage around its head.
Meanwhile the other helpers are all helping Pokémon too. James and Brock are gluing a Pinsir's pincer back on while Jessie and Misty are trying to get a Voltorb out of a Weepinbell’s mouth. The Voltorb is getting pretty mad and Dr. Proctor says it might self-destruct. Jessie can't get it out so a Chansey has a try. It is successful.
Ash, Brock and Dr. Proctor are now helping a very angry Dodrio that has its heads tangled up. Dr. Proctor says that the three heads represent joy, sorrow and anger. Ash says that they all look pretty angry to him. Dr. Proctor says they have to do something or it will suffocate. He tries to put it to sleep by giving it some anesthetic but one of the heads knocks his hand and injects the needle into the doctor. Dr. Proctor says that he will be out for 6 hours and then he goes to sleep. Ash sends out Squirtle which uses Water Gun on Dodrio. He then gets Pikachu to Thundershock it. Ash readies a Pokéball but Brock reminds him that he can't catch it.
Everyone is still busy looking after various Pokémon. Jessie and James have decided it is time for Team Rocket to take over and catch all of the Pokémon. They take off their hospital uniforms and jump up onto a stretcher. They then say their motto and at the end Meowth jumps up and says "I want my charm!" Jessie and James fall to the floor. Jessie says that it is time to catch all of the Pokémon. Misty replies saying that we all help your Pokémon is that the right thing to do now? Jessie says yes. Jessie and James then push stretcher catchers at Ash, Misty and Brock. These are stretchers with arms. They catch all three of them. James pulls out a big needle and says he is going to use it on Ash, but a Chansey jumps in front of him. James tells it to move but it won't. He then calls to Arbok to get rid of it. Arbok doesn't move so James calls to Weezing but it won't attack either. Dr. Proctor wakes up and says that they won't attack Chansey because it helped to treat them. Jessie gets angry at him and throws a beaker of water at him but Dr. Proctor whips out a scalpel and cuts it in half. He then reveals his 'ammo' a coat lined with scalpels, needles and scissors. James says to Jessie that they better not mess with him. Some Chansey free Ash and friends and they push the stretchers at Team Rocket, who run out of the building. Jessie is annoyed that they didn't get any Pokémon, but James says they did get one. He holds out a Voltorb which self-destructs in his hand. When they land on the ground again, the charm that was embedded in Meowth’s head pops back out again. He’s very relieved, but Jessie and James don’t exactly agree.
Back in the hospital Dr. Proctor says that Ash , Misty and Brock should be doctors and he asks them if they want to stay and train. They decline. Misty says that she wants to be a doctor one day but for now she still has a lot to learn about water Pokémon. Ash and friends leave the hospital waving goodbye to their newfound friend Dr. Proctor.